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A whole-genome sequenced control population in northern Sweden reveals subregional genetic differences
Umeå University, Faculty of Science and Technology, Department of Chemistry. (Arcum)ORCID iD: 0000-0002-4476-9255
Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
Umeå University, Faculty of Medicine, Department of Radiation Sciences, Oncology.ORCID iD: 0000-0002-6754-2571
Umeå University, Faculty of Social Sciences, Centre for Demographic and Ageing Research (CEDAR). (Arcum)ORCID iD: 0000-0002-2014-7179
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2020 (English)In: PLOS ONE, E-ISSN 1932-6203, Vol. 15, no 9, article id e0237721Article in journal (Refereed) Published
Abstract [en]

The number of national reference populations that are whole-genome sequenced are rapidly increasing. Partly driving this development is the fact that genetic disease studies benefit from knowing the genetic variation typical for the geographical area of interest. A whole-genome sequenced Swedish national reference population (n = 1000) has been recently published but with few samples from northern Sweden. In the present study we have whole-genome sequenced a control population (n = 300) (ACpop) from Västerbotten County, a sparsely populated region in northern Sweden previously shown to be genetically different from southern Sweden. The aggregated variant frequencies within ACpop are publicly available (DOI 10.17044/NBIS/G000005) to function as a basic resource in clinical genetics and for genetic studies. Our analysis of ACpop, representing approximately 0.11% of the population in Västerbotten, indicates the presence of a genetic substructure within the county. Furthermore, a demographic analysis showed that the population from which samples were drawn was to a large extent geographically stationary, a finding that was corroborated in the genetic analysis down to the level of municipalities. Including ACpop in the reference population when imputing unknown variants in a Västerbotten cohort resulted in a strong increase in the number of high-confidence imputed variants (up to 81% for variants with minor allele frequency < 5%). ACpop was initially designed for cancer disease studies, but the genetic structure within the cohort will be of general interest for all genetic disease studies in northern Sweden.

Place, publisher, year, edition, pages
Public Library Science , 2020. Vol. 15, no 9, article id e0237721
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Medical Genetics
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URN: urn:nbn:se:umu:diva-175837DOI: 10.1371/journal.pone.0237721ISI: 000571887500123PubMedID: 32915809Scopus ID: 2-s2.0-85090917774OAI: oai:DiVA.org:umu-175837DiVA, id: diva2:1477023
Available from: 2020-10-16 Created: 2020-10-16 Last updated: 2023-03-23Bibliographically approved

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Svensson, DanielRentoft, MatildaDahlin, Anna M.Lundholm, EmmaSjödin, AndreasMelin, Beatrice S.Trygg, JohanJohansson, Erik

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Svensson, DanielRentoft, MatildaDahlin, Anna M.Lundholm, EmmaSjödin, AndreasMelin, Beatrice S.Trygg, JohanJohansson, Erik
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Department of ChemistryDepartment of Medical Biochemistry and BiophysicsOncologyCentre for Demographic and Ageing Research (CEDAR)
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